Convert armatures to empties while retaining animation data
If I got you correctly you may transfer the animation data from bones to empties and then bake it to keyframes.

Add an Empty in the same location as keyframed bone and give it a Copy Transforms constraint. Set the Head/Tail value to 0.500 to place it in the middle of a bone.


Select an Empty, go to the Animation bookmark of a Tool Shelf (T) and press the Bake Action button. Check all the checkboxes there and set the Object as a bake data type. Delete the bone finally.